What has not been done so far is look at overlap across all 3 groups above. How can we bring all these efforts together? Are there other efforts to do the same out there? e.g. have NCATS tried to do this?

But the question still resonates WHY?

Why do these 3 groups ‘have to’ collate the molecules?

Why could the NCATS initiative have not posted the molecules on the website or linked to them in PubChem in the first place (would have taken no effort for each company to provide a structure)?

Why did they get groups to propose repurposing the molecules without disclosing molecule structures?

Why is computational analysis not at the forefront of the repurposing efforts before spending experimental resources?

Why oh why did someone not think of this, or did they?

Its not like people have not proposed how to do this kind of thing before.

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I just don’t get why funding was put into the project (and likely a big chunk of money) but no effort put into preparing the SDF file for the community ahead of time. No..instead, anyone interested in computational work has to do all the work to aggregate the data. And that will happen many times. ONE group, the host, should have done the work and asked the rest of us to annotate/curate if we found issues.

sean says:

Many thanks Tony.
Based on who put this dataset together it surprises me that there was not even a note as to why structures were not put up. Was it because pharma would not let them, was it because they were afraid we would all rush and generate predictions with models and then they would be inundated with grant proposals? Who knows.

Again the crowd is doing the work of a govt organization..and not getting paid for it.

sean says:

Wouldn’t-it-be-nice-if organizations with advanced development candidates published med chem papers, according to MIABE guidelines, where a) the IUPAC string was in direct proximity to the code number in the PubMed abstract (especially for subscriptions journal) b) cited their patent numbers in the article c) submitted the structures to PubChem and ChemSpider (thereby ensuring they were correct off the bat, d) at least check that MeSH had picked up the link correctly and LBNL ensure that ChEMBL curated the paper and captured the assay data that , in turn, went into PubChem Bioassay.